ArticleNature communications2021
Fast alignment and preprocessing of chromatin profiles with Chromap.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
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Who cites it
166 citing papers in PubMed.
- Identification of Genome-Wide Chromatin Structural Aberration in Cancer by Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Near-complete assembly of wild emmer wheat unveils centromere reorganization during polyploid evolution.Nature genetics · 2026Article
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
- KDM6A loss enhances oxidative phosphorylation uncovering tissue-level convergent evolution.The EMBO journal · 2026Article
- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.G3 (Bethesda, Md.) · 2026Article
- Telomere-to-telomere genome ofHorticulture research · 2026Article
- From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.Molecular biology and evolution · 2026Article
- Chromosome-Scale Genome of Zoonotic EyewormAnimals : an open access journal from MDPI · 2026Article
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
- Ultra-sensitive profiling of CRISPR-Cas off-target effects with Tracking-seq2.Nature communications · 2026Article
- Single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq).Nature protocols · 2026Review
- Human Alu loci gain enhancer-type epigenetic modifications in monocytes during response to bacterial LPS.Epigenetics & chromatin · 2026Article
- Chromosome-level genome of the Adriatic sturgeon, Acipenser naccarii: A resource for polyploid fish genomics.The Journal of heredity · 2026Article
- Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian.Nature ecology & evolution · 2026Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Chromosome-level genome assembly of the jumping spider Spartaeus platnicki.Scientific data · 2026Article
- A telomere-to-telomere gapfree genome assembly of Triplophysa stoliczkae (Tibetan stone loach, family Nemacheilidae).Scientific data · 2026Article
- Protocol update to: Genome-wide interrogation of protein-DNA interactions in mammalian cells using ChIPmentation.STAR protocols · 2026Article
106 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics' CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.
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